I Was Always Here
by BecauseMarvelJustRocks
Summary: Skye is- unknown to her- an 084. She doesn't tell anyone that she can turn invisible, no, that would get her in trouble. But after finding a Family in Coulson's team, she thinks that, maybe, it won't be so bad. Of course, she wants to date that Bio Chem scientist as well. 084!Skye, Skimmons, Family!Team
1. Some people can be ordinary

**I do not own Agents of S.H.I.E.L.D. All rights go to Marvel.**

The first time that it happened was an accident.

She was nine and had just been sent back to the Saint Agnes Orphanage. She had really thought that the Brodys would be the family, too. But just like all at the others, she "wasn't a good fit".

After she got back, she just wanted to be alone. She sat on her bed in her room, one that she shared with another two girls. They weren't here right now, doing chores- she had been left off because she had just got back.

She wanted to hide, to be alone, to never be seen. She was a failure, someone that people would never like. She crept onto her bed, staying quiet, waiting for sleep.

"Skye, darling? Where are you?" She heard Sister Jones' voice call from the hallway, her head poked into the room. She turned around, as if to leave, and Skye called out.

"Sister Jones? I'm right here."

"Oh Skye darling, I must have missed you under the blanket." Skye thought that was odd. She hadn't been under the blanket- on top of it, in fact. "Come now, it's time for dinner."

So, that first time, Skye passed Sister Jones not seeing her off as a coincident.

She had no idea how wrong she was.

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The second time, she was thirteen.

She had been to another few foster homes over the years, but she hadn't stayed at them any longer than two weeks.

She had gotten into trouble after school- yelling at some bullies as they were cornering some poor kid. They had chased after her, and as she turned around a corner, she saw a side alley. Perfect. She hid behind a dumpster, hoping to whoever was up there that she wasn't caught.

They had literally walked right up to the spot where she hid, searching for the little kid the stopped them from having some "fun".

"Come on man, she's not here. Let's just go find some little nerd to beat up." That was one of the followers, she though. One of the nicer ones... Not that they were nice anyway.

"Yeah, I guess... But next time I see her," The leader punched his palm. "She's going down."

As they walked away Skye wondered what had just happened. She wasn't stupid- she knew that they should of seen her, in the obvious spot place that she was. But they didn't.

She remembered it this time.

And someday, she was going to find out why they ignored her. What made her special.

She didn't know how much of her future she had just changed.

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She though about it over the years- about how when she really needed to go away, to disappear, she did.

_She could turn invisible._

Of course, she couldn't do it consciously. Yet. She would find a way, any way, to make this work.

She did.

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By the time that she was seventeen, she could do it almost effortlessly.

Of course, Skye never did it in front of anyone, or told anyone, or even practiced near a living soul.

She knew what _they_ did to people that were thought as strange.

So when the scary men in dark suits found her, at 27, she was understandably worried.

Very, very worried.


	2. I won't let you die

**I do not own Agents of S.H.I.E.L.D. All rights go to Marvel.**

Luck, it turned out, was on her side.

Agent Coulson had brought her in because she was a part of the Rising Tide. She wasn't going to deny that- hacking was her life, and she was proud of it. But it made her worry. Was she under surveillance now? Did they have someone watching her every move? Would her secret- the most powerful and well kept secret of her life- remain safe?

She was pretty sure that they knew everything that she did- she was part of there team now, accepting Coulson's offer as she did.

And Skye had to admit, there were certain perks to staying on "the Bus". Like not having to worry about running out of food or being caught by the police- because technically, that had already happened. And that cute girl down in the lab- Simmons, her name was- wasn't bad eye candy either.

She probably didn't swing that way, though. Sigh. Another disappointment in the life of Skye.

She could get used to this team- with their unusual habits and (for FitzSimmons, a least) love of words so long that she probably couldn't count all the letters in them. They were- as much as she hated to admit it- becoming a family to her. And while, deep down inside, she knew that she desired a family... She wasn't sure if she really wanted one.

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She was going to do it, Skye told herself. Jemma only had a few hours to live. Skye wasn't going to just let her leave her life like everyone else she had loved. Especially without knowing how Skye thought about her- bar the M rated stuff, of course.

She just didn't- as stupid as it sounds- know how to phrase it. But then Skye though _'Oh hell, it's not like she's going to be here for much longer. I'll tell it to her straight._' She walked down the spiral stairs- making sure that Ward wasn't in the little gym set up first- and approached the row of glass widows barring her entrance to the lab.

FitzSimmons were bustling about, working harder than usual- Skye reasoned it was because Jemma was infected with an alien disease that caused its victims to float a meter and a half of the ground before sending out an EMP blast with enough power to send this whole plane and it's inhabitants crashing to their deaths. Not that she would say that out loud, no- she absolutely did not want to make this situation any worse. She pushed open the door and made her way over to her- dare she say it- crush.

On the bench top she saw a floating mouse in a cage- obviously a test subject for the cure that they were working on. There was discarded pieces of equipment everywhere- wires, syringes, even a ammunition clip. As she approached the table, head down, she heard a body hit the floor. Fearing the worse, Skye ran over- only to see that Simmons had knocked Leo out.

"Er, Skye, what are you doing here? You need to leave, it's not safe. I need to be alone now, before I, I..." Jemma whimpered "I blow."

"Jemma." She was unresponsive. "Jem, look at me." Skye said gently, reaching out to her. She put a hand under Jemma's chin, tilting her head up to face her. "Look. You are the smartest person I know. You have two doctorates in fields I can't pronounce, put up with Fitz for a living and love homework more than life itself. If you can't cure this thing, then no one can. You just need to focus."

"No Skye, I can't. We've tried everything, every compound, every formula, calculated each variable and how long it will take for us to reach somewhere safe. There's no choice. I have to get off this plane or every one, Fitz, Coulson, May, Ward, and you are going to die... And I can't have that happen." She didn't see Skye's startled eyes. "Just, please, let me do this."

"Let me give you a reason not to."

Because Skye, as much as she loved this little family, this group that had come together, couldn't stand it if one of them was missing. Especially not her Jemma.

So she leant forward and pressed her lips to Jemma's, hoping that this would be the thing needed to save the one person most important to her.


	3. Now you see me

**I do not own Agents of S.H.I.E.L.D. All rights go to Marvel.**

It turned out that everything would be okay.

Well, there had been a little confusion at first. Jemma was rather surprised that someone was kissing her, a girl no less- but since it was her crush, she had no problems with it.

They agreed to wait until no one's life was in immediate danger before having a little "talk". There was also the added incentive that Skye had promised her a "reward" once she has found a cure. If what had happened earlier was anything to go by, Jemma was pretty sure that she would like it.

After waking up a rather pissed off Leo, Skye sat down on a stool and watched the duo called "FitzSimmons" work. It was quite amazing, really. They were in perfect sync, knowing exactly what the other was thinking, what they were doing, understanding the reasoning and cause behind each movement.

It made her jealous of Fitz, really.

He _knew _Jemma like no other- her personality, what she liked, her favourite foods and things. Skye wanted that connection. Jemma was her's, and no alien virus, best friend, or S.H.I.E.L.D. inter-office relationship policy was going to take her away.

She didn't know that she could be so possessive.

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Two hours after being injected with the antidote, Simmons hadn't exploded. They hoped that was a good thing.

But now came the moment the Skye had been both waiting for and dreading. Talking with Jemma.

They sat on Skye's bed, in her "pod"- their personal areas were too small to be accurately be called rooms- and Jemma had her head lying on Skye's shoulder. Skye wrapped her arms around her, pulling the girl closer.

"I've liked you for a while now," Jemma whispered in the ear. "I didn't think that you would feel the same way."

Skye was quiet for a minute, before she chuckled. "Well, I would be a fool not to like you." Jemma blushed, and Skye smirked. "Besides, I'm rather good at hiding things when I want to."

"Oh, really? I suppose that's why you were so forward when you kissed me. And why I am practically sitting on your lap, and the reason-" She was cut off by Skye's lips on hers.

"You talk to much."

Three minutes later, Skye pulled back to see a very flustered and blushing Simmons. Jemma thought it was embarrassing. Skye just thought that it made her cuter- although she _was _rather biased.

"Where does this put us now?" The taller girl asked her.

I think that, for the moment, we best keep this from the team. You know how Coulson and Ward are about protocol. But," Skye leant forward and placed a small kiss on Jemma's check, "I would be more than happy to date you on secret."

Jemma smiled, hugging Skye. They would find a way to make this work.

"Okay then. Next landing, you and me are going for a 'Girls night out' " Jemma grinned mischievously. "We can tell each other about our crushes, and what we like about them."

Skye laughed, before kissing her again.

Jemma was okay with that.

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She had't thought that anyone from the team would find out this soon.

Or that she would see one of _them _again.

Skye had run into the gang a few years ago, when she was still on the run. One of them had seen her mid-visibility. It had still taken Skye a few seconds to change back then, and someone had walked in on her at the worst moment.

They had offered to "hire" her. She didn't want a job though. Especially not that kind of one. At her refusal, they had locked her up. She escaped relatively easy, of course.

But they had evidently not stopped looking for her.

And of course, the plane just _had _to stop in New York.

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She was on a date with Jemma- their first, in fact. Skye was glad that they were finally going out. One could only wait for a certain amount of time without doing something befo having to do it.

At least she could kiss Jemma in somewhat privacy.

They had just began eating when the thug walked into the restaurant. Looking around, his eyes caught Skye's and widened. He immediately whipped out his phone and began calling some one. _'Probably his boss.' _Skye thought.

"We're leaving." Skye said to Jemma. She tossed some money on the table and grabbed Jemma's wrist, dragging her out the back entrance.

"Skye, what are you doing? We just got here, we can't leave so soon. And what about our date?" Jemma looked so disappointed, it almost broke Skye's heart.

"Jemma, look. See that guy over there?" Skye pointed at him and Jemma nodded. "Okay. His boss had been searching for me for the last five years." Jemma gave her a startled look. "I got into trouble after doing a hack for him. We need to leave this restaurant now, before his back-up gets here."

As they headed for the door, the thug saw them and followed. The back door lead to a side alley, and the car was parked around the corner. They were halfway there when the man pulled out a gun and shot at the pair.

The bullet went straight over them, but that didn't stop them from ducking to the floor.

"Shit!" Skye exclaimed, before- in Jemma's eyes- vanishing.

"Skye? Where are you?" Jemma wondered where she had gone. There weren't any bins ar things that she could of hid behind. It was like she had turned invisible.

."Jemma, get to the car. I'll meet you there. Just get away from here!" Not bothering to wonder where Skye's voice had come from, Jemma ran to the car.

Meanwhile, Skye invisibily approached the thug. He was constantly moving, not staying still incase she appeared again.

"Boo!" He heard, before something ripped the gun out of his hand and it flew into the wall. Skye pulled her emergency night-night gun out of her bag before shooting him in the chest with it. As the body hit the ground, Skye ran after Jemma to the car.

Just as they left, another group of men got to the alley.

"Damn it!"

**AN:**

**Any questions or theories on what is going to happen next? I really appreciate all the people who have followed or favourited this story (Which is my first, by the way). Do you want longer chapters and updates or shorter? And who can guess what Skye's second power is?**

**-BecauseMarvelJustRocks**


	4. Let Me Be With You

**I don't own Agents of S.H.I.E.L.D. All rights go to Marvel.**

**Shoutout to 'XJ0461', 'f00f00', 'TheMajesticLauren' and 'Salkri Kachemench'. Thanks to Grammar Nazi Bot 3000 for Beta-ing.**

Jemma had hardly said a word to her since the incident.

And while she was a little saddened, Skye really couldn't blame her. Your first attempted kidnapping was quite a lot to take in.

After leaving the alley, they has stopped at a drive through to state their need for caffeine before continuing onto the bus. Jemma had not minded having coffee instead of tea for once, needing a hot beverage. Afterwards she had silently moved into her bedroom, seemingly in shock. When Coulson asked Skye what happened, she just said that 'Someone attempted to mug us.' and that 'I took him out.'

At Phil's alarmed look, Skye reassured him that she had only used the night night gun.

Now though, after everyone was asleep, (or at least in their rooms) Skye had knocked on Jemma's open door and proclaimed,

"I brought ice cream!"

Skye sat down next to the scientist and offered her a spoon.

"It's comfort food. You like choc chip, right?" At Jemma's silent nod, Skye sighed.

"Look, Jemma, I know it's a lot to take in," The girl shot her a 'really' look, "But the easiest way to get over it is to talk to someone."

It was a few minutes before Simmons spoke.

"Why is he after you, Skye?" She asked in a soft tone. "And don't give me bullshit about some hack. I know that your better than being caught for messing up a deal."

"I... It's complicated, Jemma." The expression she received told her that it wasn't an acceptable answer. "I'm different. That's why I had you leave the alley. I didn't want you to think that I'm a freak."

Skye held her arm up, then made her hand disappear. Jemma let out a soft gasp. "I could do it since I was little. Your the first person that I have willingly told. I'll understand if you don't want to be on the team anymore." Her voice drifted of and she turned away.

She was suddenly turned back around and slapped on the shoulder.

"Skye! How dare you think such a thing. Being different isn't a bad thing. It takes courage to tell someone about this, and I respect you for that. But I never want to hear you degrade yourself like that again. Understand?"

Skye didn't answer, simply leaning her head into Jemma's shoulder and wrapping her arms around her. She responded in kind. After a few minutes of listening to her tearless sobs, Jemma pushed her off.

"You brought ice cream, right?" Skye nodded and picked the tub up off the floor. "Then let's watch a movie. We didn't exactly get to do anything earlier, did we?"

Skye smiled, suddenly feeling a lot better. A date with a beautiful girl (especially one that happened to be into you) would do that to a person.

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Coulson woke them up the next morning from each others arms.

While Jemma blushed, Skye yawned and shamelessly pulled her closer.

"Be up in twenty, girls. We're going to the Hub. Simmons, I need you to retrieve some intel from Agent Shaw. He has, ah... placed it up his nasal cavity."

If Jemma hadn't been awake before, she definitely was now. Skye made a face.

"Why would someone even do that? I mean, you robot people do some pretty weird shit, but shoving stuff up your nose? Do they understand the meaning of the word hygiene?"

Jemma stifled at laugh while Coulson smiled.

"Don't even start, Skye. I've had friends doing way worse than that for the success of a mission."

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"I hope you know what your doing, Jemma." Skye said.

"Don't be ridiculous. As long as Agent Shaw doesn't breathe, we'll be fine." She hastily turned to the agent in question and rephrased her statement. "That was a joke. You should, of course, feel comfortable breathing, just not through your nose. And very minimally through your mouth."

"That's all the intel you recovered?" Asked Coulson.

Shaw replied with "I certainly hope so. No offence doc, but that was rather... irritating."

"Well thank you, Agent Shaw, for keeping it safe up there." Jemma walked over to another bench to remove the snot.

"We'll forward this to the Hub. Data and Info will get whatever we need out of it. In fact, we're headed there now to drop you off."

"The Hub? Really? How exciting." Jemma exclaimed.

"It's been ages." Leo agreed.

"Do you indeed me to analyse the data?" Skye asked.

"That won't be necessary."

"If it's encrypted, I can mine the chip for him."

"I'm afraid this mission is classified. Clearance level eight."

"Oh."

"Ah."

"Wait, what? He can just shut us out of the process like that?"

"Well, he did say that the mission is level eight." Jemma reminded her.

"And of course, we're not, so we can't know about it." Leo said in his Scottish accent.

"Right, but this is normally the part where we all stand around the holotable and learn about stuff? I mean, aren't we all on the same team?"

"No need to get started on one of your socialist riffs."

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"S.H.I.E.L.D.'s whole infrastructure is based on the hierarchy and compartmentalisation of intelligence. Every agent can have intel on a mission, Skye. It makes the organisation vulnerable."

"Okay, fine, but if I had just caught my way out of a Siberian prison, I'd kind of want to know what for."

"Coulson's got you used to the plane, the way we do things here." Shaw said. "The Hub is different."

"The Hub? What's the Hub?"

"Buckle up, guys." May said over the intercom. "We touchdown in five."

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"That is the Hub, Skye."

"Wow. I never realised Big Brother was so... Big." She was silent for a minute, taking it in.

"Oh, this is nothing." Jemma said excited. "Wait until you see the Triskelion."

"Everyone's wearing the same suit. Can some one tell me why, please? And the badges. Do I get a badge? I want a badge."

"That's your badge." Coulson said, tapping her wrist bracelet. "You still have a long way to go before you even hit level one."

A bald man walked up to them.

"Agent Sitwell."

"Agent Coulson. Good to see you feeling better. Agent Hand is waiting for you in the situation room."

"And she doesn't like to wait."

"You know her?"

"Just her reputation." They walked further down the hall. "After you."

"Your level sevens can join us in the briefing. Say cheese." Coulson, May, Ward and Sitwell took turns leaning forward to have their retina scanned.

"Is this your subtle way of saying we can't come with?" Skye asked.

"We'll be back. Fitz, Simmons, keep an eye on Skye. I don't want her wondering off somewhere she shouldn't be."

"Ah... We should probably head to the tech corridor."

"Oh, I can't wait to see the new chem-kit."

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"Agent Coulson."

"Agent Hand."

"Good to finally be able to put a face to the name."

"Likewise."

"This is Agent May and Agent Ward." Coulson said. They nodded their heads respectively.

"Well now that we've got that out of the way, here's what you can know. The intel you retrieved from Agent Shaw tells us that a separatist group in South Ossetia has build a weapon called 'ezbiitomet' "

"The 'Overkill Device?' " Ward asked.

"A little overdramatic for my tastes. We've intercepted chatter that tells us they plan to use the weapon in the next 24 hours to declare their independence from Russia and Georgia. We believe it creates sonic vibrations powerful enough to trigger weapons from a great distance- anything from the missiles on a helicopter to a nuclear warhead sitting in its silo."

"So if we move on them, they could use our own weapons against us."

"Exactly. That's why I need a two-man team to sneak across the disputed border undetected, break into the separatist stronghold, and disable the weapon in the next 24 hours. And you have two people who fit my bill."

"Not a problem." Ward told her. "I was in Georgia during the incursion of '08. I still have contacts on the South Ossetian border."

"And you'll have to use them. But, we don't have specs on the device, so I need someone on the team who can identify and dismantle it on-site."

"Does she mean..." Coulson began.

Ward answered the unspoken sentence. "I think she does."

**AN: I really haven't updated in a while, have I? Skye Stark will be up in a few hours and I remind (and ask) you all to suggest what Skye's second ability will be. Votes will be tallied and the highest by chapter eight will be included. If there are less then five for one power I will put mine in.**

**-BecauseMarvelJustRocks**


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